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commit: d199c2134722aeb381c495e6ddc0f8adee06386f |
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Author: Alexey Shvetsov <alexxy <AT> gentoo <DOT> org> |
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AuthorDate: Thu May 14 14:03:22 2020 +0000 |
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Commit: Alexey Shvetsov <alexxy <AT> gentoo <DOT> org> |
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CommitDate: Thu May 14 14:03:22 2020 +0000 |
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URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=d199c213 |
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|
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sci-chemistry/gromacs: drop 2019.9999 and 2018.9999 |
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|
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Package-Manager: Portage-2.3.99, Repoman-2.3.22 |
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Signed-off-by: Alexey Shvetsov <alexxy <AT> gentoo.org> |
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|
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sci-chemistry/gromacs/gromacs-2018.9999.ebuild | 295 ----------------------- |
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sci-chemistry/gromacs/gromacs-2019.9999.ebuild | 316 ------------------------- |
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2 files changed, 611 deletions(-) |
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|
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diff --git a/sci-chemistry/gromacs/gromacs-2018.9999.ebuild b/sci-chemistry/gromacs/gromacs-2018.9999.ebuild |
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deleted file mode 100644 |
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index 4db9e9672b0..00000000000 |
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--- a/sci-chemistry/gromacs/gromacs-2018.9999.ebuild |
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+++ /dev/null |
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@@ -1,295 +0,0 @@ |
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-# Copyright 1999-2019 Gentoo Authors |
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-# Distributed under the terms of the GNU General Public License v2 |
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- |
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-EAPI=7 |
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- |
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-CMAKE_MAKEFILE_GENERATOR="ninja" |
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- |
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-inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo-r1 toolchain-funcs xdg-utils |
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- |
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-if [[ $PV = *9999* ]]; then |
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- EGIT_REPO_URI="git://git.gromacs.org/gromacs.git |
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- https://gerrit.gromacs.org/gromacs.git |
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- https://github.com/gromacs/gromacs.git |
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- https://repo.or.cz/r/gromacs.git" |
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- [[ $PV = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:4}" |
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- inherit git-r3 |
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-else |
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- SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz |
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- test? ( http://gerrit.gromacs.org/download/regressiontests-${PV/_/-}.tar.gz )" |
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- KEYWORDS="~amd64 ~arm ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" |
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-fi |
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- |
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-ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2" |
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- |
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-DESCRIPTION="The ultimate molecular dynamics simulation package" |
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-HOMEPAGE="http://www.gromacs.org/" |
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- |
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-# see COPYING for details |
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-# https://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING |
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-# base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib |
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-LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )" |
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-SLOT="0/${PV}" |
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-IUSE="X blas cuda +doc -double-precision +fftw +hwloc lapack mkl mpi +offensive opencl openmp +single-precision test +threads +tng ${ACCE_IUSE}" |
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- |
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-CDEPEND=" |
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- X? ( |
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- x11-libs/libX11 |
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- x11-libs/libSM |
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- x11-libs/libICE |
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- ) |
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- blas? ( virtual/blas ) |
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- cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 ) |
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- opencl? ( virtual/opencl ) |
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- fftw? ( sci-libs/fftw:3.0 ) |
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- hwloc? ( <sys-apps/hwloc-2 ) |
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- lapack? ( virtual/lapack ) |
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- mkl? ( sci-libs/mkl ) |
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- mpi? ( virtual/mpi ) |
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- " |
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-BDEPEND="${CDEPEND} |
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- virtual/pkgconfig |
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- doc? ( |
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- app-doc/doxygen |
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- dev-texlive/texlive-latex |
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- dev-texlive/texlive-latexextra |
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- media-gfx/imagemagick |
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- )" |
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-RDEPEND="${CDEPEND}" |
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- |
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-REQUIRED_USE=" |
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- || ( single-precision double-precision ) |
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- cuda? ( single-precision ) |
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- cuda? ( !opencl ) |
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- mkl? ( !blas !fftw !lapack )" |
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- |
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-DOCS=( AUTHORS README ) |
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- |
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-RESTRICT="!test? ( test )" |
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- |
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-if [[ ${PV} != *9999 ]]; then |
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- S="${WORKDIR}/${PN}-${PV/_/-}" |
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-fi |
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- |
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-pkg_pretend() { |
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- [[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs" |
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- use openmp && ! tc-has-openmp && \ |
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- die "Please switch to an openmp compatible compiler" |
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-} |
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- |
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-src_unpack() { |
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- if [[ ${PV} != *9999 ]]; then |
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- default |
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- else |
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- git-r3_src_unpack |
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- if use test; then |
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- EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \ |
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- EGIT_BRANCH="${EGIT_BRANCH}" \ |
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- EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\ |
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- git-r3_src_unpack |
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- fi |
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- fi |
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-} |
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- |
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-src_prepare() { |
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- #notes/todos |
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- # -on apple: there is framework support |
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- |
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- xdg_environment_reset #591952 |
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- |
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- cmake-utils_src_prepare |
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- |
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- use cuda && cuda_src_prepare |
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- |
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- GMX_DIRS="" |
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- use single-precision && GMX_DIRS+=" float" |
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- use double-precision && GMX_DIRS+=" double" |
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- |
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- if use test; then |
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- for x in ${GMX_DIRS}; do |
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- mkdir -p "${WORKDIR}/${P}_${x}" || die |
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- cp -al "${WORKDIR}/regressiontests"* "${WORKDIR}/${P}_${x}/tests" || die |
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- done |
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- fi |
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- |
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- DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats" |
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- # try to create policy for imagemagik |
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- mkdir -p ${HOME}/.config/ImageMagick |
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- cat >> ${HOME}/.config/ImageMagick/policy.xml <<- EOF |
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- <?xml version="1.0" encoding="UTF-8"?> |
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- <!DOCTYPE policymap [ |
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- <!ELEMENT policymap (policy)+> |
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- !ATTLIST policymap xmlns CDATA #FIXED ''> |
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- <!ELEMENT policy EMPTY> |
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- <!ATTLIST policy xmlns CDATA #FIXED '' domain NMTOKEN #REQUIRED |
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- name NMTOKEN #IMPLIED pattern CDATA #IMPLIED rights NMTOKEN #IMPLIED |
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- stealth NMTOKEN #IMPLIED value CDATA #IMPLIED> |
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- ]> |
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- <policymap> |
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- <policy domain="coder" rights="read | write" pattern="PS" /> |
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- <policy domain="coder" rights="read | write" pattern="PS2" /> |
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- <policy domain="coder" rights="read | write" pattern="PS3" /> |
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- <policy domain="coder" rights="read | write" pattern="EPS" /> |
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- <policy domain="coder" rights="read | write" pattern="PDF" /> |
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- <policy domain="coder" rights="read | write" pattern="XPS" /> |
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- </policymap> |
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- EOF |
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-} |
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- |
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-src_configure() { |
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- local mycmakeargs_pre=( ) extra fft_opts=( ) |
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- |
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- #go from slowest to fastest acceleration |
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- local acce="None" |
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- use cpu_flags_x86_sse2 && acce="SSE2" |
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- use cpu_flags_x86_sse4_1 && acce="SSE4.1" |
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- use cpu_flags_x86_fma4 && acce="AVX_128_FMA" |
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- use cpu_flags_x86_avx && acce="AVX_256" |
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- use cpu_flags_x86_avx2 && acce="AVX2_256" |
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- |
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- #to create man pages, build tree binaries are executed (bug #398437) |
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- [[ ${CHOST} = *-darwin* ]] && \ |
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- extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF" |
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- |
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- if use fftw; then |
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- fft_opts=( -DGMX_FFT_LIBRARY=fftw3 ) |
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- elif use mkl && has_version "=sci-libs/mkl-10*"; then |
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- fft_opts=( -DGMX_FFT_LIBRARY=mkl |
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- -DMKL_INCLUDE_DIR="${MKLROOT}/include" |
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- -DMKL_LIBRARIES="$(echo /opt/intel/mkl/10.0.5.025/lib/*/libmkl.so);$(echo /opt/intel/mkl/10.0.5.025/lib/*/libiomp*.so)" |
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- ) |
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- elif use mkl; then |
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- local bits=$(get_libdir) |
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- fft_opts=( -DGMX_FFT_LIBRARY=mkl |
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- -DMKL_INCLUDE_DIR="$(echo /opt/intel/*/mkl/include)" |
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- -DMKL_LIBRARIES="$(echo /opt/intel/*/mkl/lib/*${bits/lib}/libmkl_rt.so)" |
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- ) |
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- else |
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- fft_opts=( -DGMX_FFT_LIBRARY=fftpack ) |
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- fi |
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- |
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- mycmakeargs_pre+=( |
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- "${fft_opts[@]}" |
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- -DGMX_X11=$(usex X) |
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- -DGMX_EXTERNAL_BLAS=$(usex blas) |
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- -DGMX_EXTERNAL_LAPACK=$(usex lapack) |
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- -DGMX_OPENMP=$(usex openmp) |
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- -DGMX_COOL_QUOTES=$(usex offensive) |
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- -DGMX_USE_TNG=$(usex tng) |
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- -DGMX_BUILD_MANUAL=$(usex doc) |
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- -DGMX_HWLOC=$(usex hwloc) |
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- -DGMX_DEFAULT_SUFFIX=off |
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- -DGMX_SIMD="$acce" |
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- -DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/" |
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- -DBUILD_TESTING=$(usex test) |
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- -DGMX_BUILD_UNITTESTS=$(usex test) |
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- ${extra} |
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- ) |
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- |
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- for x in ${GMX_DIRS}; do |
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- einfo "Configuring for ${x} precision" |
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- local suffix="" |
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- #if we build single and double - double is suffixed |
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- use double-precision && use single-precision && \ |
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- [[ ${x} = "double" ]] && suffix="_d" |
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- local p |
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- [[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF" |
219 |
- local cuda=( "-DGMX_GPU=OFF" ) |
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- [[ ${x} = "float" ]] && use cuda && \ |
221 |
- cuda=( "-DGMX_GPU=ON" ) |
222 |
- local opencl=( "-DGMX_USE_OPENCL=OFF" ) |
223 |
- use opencl && opencl=( "-DGMX_USE_OPENCL=ON" ) cuda=( "-DGMX_GPU=ON" ) |
224 |
- mycmakeargs=( |
225 |
- ${mycmakeargs_pre[@]} ${p} |
226 |
- -DGMX_MPI=OFF |
227 |
- -DGMX_THREAD_MPI=$(usex threads) |
228 |
- "${opencl[@]}" |
229 |
- "${cuda[@]}" |
230 |
- "$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")" |
231 |
- -DGMX_BINARY_SUFFIX="${suffix}" |
232 |
- -DGMX_LIBS_SUFFIX="${suffix}" |
233 |
- ) |
234 |
- BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure |
235 |
- [[ ${CHOST} != *-darwin* ]] || \ |
236 |
- sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die |
237 |
- use mpi || continue |
238 |
- einfo "Configuring for ${x} precision with mpi" |
239 |
- mycmakeargs=( |
240 |
- ${mycmakeargs_pre[@]} ${p} |
241 |
- -DGMX_THREAD_MPI=OFF |
242 |
- -DGMX_MPI=ON |
243 |
- -DGMX_OPENMM=OFF |
244 |
- -DGMX_BUILD_MDRUN_ONLY=ON |
245 |
- -DBUILD_SHARED_LIBS=OFF |
246 |
- -DGMX_BUILD_MANUAL=OFF |
247 |
- "${opencl[@]}" |
248 |
- "${cuda[@]}" |
249 |
- -DGMX_BINARY_SUFFIX="_mpi${suffix}" |
250 |
- -DGMX_LIBS_SUFFIX="_mpi${suffix}" |
251 |
- ) |
252 |
- BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_src_configure |
253 |
- [[ ${CHOST} != *-darwin* ]] || \ |
254 |
- sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}_mpi/gentoo_rules.cmake" || die |
255 |
- done |
256 |
-} |
257 |
- |
258 |
-src_compile() { |
259 |
- for x in ${GMX_DIRS}; do |
260 |
- einfo "Compiling for ${x} precision" |
261 |
- BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
262 |
- cmake-utils_src_compile |
263 |
- # not 100% necessary for rel ebuilds as available from website |
264 |
- if use doc; then |
265 |
- BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
266 |
- cmake-utils_src_compile manual |
267 |
- fi |
268 |
- use mpi || continue |
269 |
- einfo "Compiling for ${x} precision with mpi" |
270 |
- BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\ |
271 |
- cmake-utils_src_compile |
272 |
- done |
273 |
-} |
274 |
- |
275 |
-src_test() { |
276 |
- for x in ${GMX_DIRS}; do |
277 |
- BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
278 |
- cmake-utils_src_make check |
279 |
- done |
280 |
-} |
281 |
- |
282 |
-src_install() { |
283 |
- for x in ${GMX_DIRS}; do |
284 |
- BUILD_DIR="${WORKDIR}/${P}_${x}" \ |
285 |
- cmake-utils_src_install |
286 |
- if use doc; then |
287 |
- newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf" |
288 |
- fi |
289 |
- use mpi || continue |
290 |
- BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \ |
291 |
- cmake-utils_src_install |
292 |
- done |
293 |
- |
294 |
- if use tng; then |
295 |
- insinto /usr/include/tng |
296 |
- doins src/external/tng_io/include/tng/*h |
297 |
- fi |
298 |
- # drop unneeded stuff |
299 |
- rm "${ED}"/usr/bin/GMXRC* || die |
300 |
- for x in "${ED}"/usr/bin/gmx-completion-*.bash ; do |
301 |
- local n=${x##*/gmx-completion-} |
302 |
- n="${n%.bash}" |
303 |
- cat "${ED}"/usr/bin/gmx-completion.bash "$x" > "${T}/${n}" || die |
304 |
- newbashcomp "${T}"/"${n}" "${n}" |
305 |
- done |
306 |
- rm "${ED}"/usr/bin/gmx-completion*.bash || die |
307 |
- readme.gentoo_create_doc |
308 |
-} |
309 |
- |
310 |
-pkg_postinst() { |
311 |
- einfo |
312 |
- einfo "Please read and cite:" |
313 |
- einfo "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). " |
314 |
- einfo "https://dx.doi.org/10.1021/ct700301q" |
315 |
- einfo |
316 |
- readme.gentoo_print_elog |
317 |
-} |
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|
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diff --git a/sci-chemistry/gromacs/gromacs-2019.9999.ebuild b/sci-chemistry/gromacs/gromacs-2019.9999.ebuild |
320 |
deleted file mode 100644 |
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index b3fc105b550..00000000000 |
322 |
--- a/sci-chemistry/gromacs/gromacs-2019.9999.ebuild |
323 |
+++ /dev/null |
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@@ -1,316 +0,0 @@ |
325 |
-# Copyright 1999-2020 Gentoo Authors |
326 |
-# Distributed under the terms of the GNU General Public License v2 |
327 |
- |
328 |
-EAPI=7 |
329 |
- |
330 |
-CMAKE_MAKEFILE_GENERATOR="ninja" |
331 |
- |
332 |
-PYTHON_COMPAT=( python2_7 ) |
333 |
- |
334 |
-inherit bash-completion-r1 cmake-utils cuda eutils multilib python-single-r1 readme.gentoo-r1 toolchain-funcs xdg-utils |
335 |
- |
336 |
-if [[ $PV = *9999* ]]; then |
337 |
- EGIT_REPO_URI="git://git.gromacs.org/gromacs.git |
338 |
- https://gerrit.gromacs.org/gromacs.git |
339 |
- https://github.com/gromacs/gromacs.git |
340 |
- https://repo.or.cz/r/gromacs.git" |
341 |
- [[ $PV = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:4}" |
342 |
- inherit git-r3 |
343 |
-else |
344 |
- SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz |
345 |
- test? ( http://gerrit.gromacs.org/download/regressiontests-${PV/_/-}.tar.gz )" |
346 |
- KEYWORDS="~amd64 ~arm ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" |
347 |
-fi |
348 |
- |
349 |
-ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2" |
350 |
- |
351 |
-DESCRIPTION="The ultimate molecular dynamics simulation package" |
352 |
-HOMEPAGE="http://www.gromacs.org/" |
353 |
- |
354 |
-# see COPYING for details |
355 |
-# https://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING |
356 |
-# base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib |
357 |
-LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )" |
358 |
-SLOT="0/${PV}" |
359 |
-IUSE="X blas cuda +doc -double-precision +fftw +gmxapi +hwloc lapack +lmfit mkl mpi +offensive opencl openmp +single-precision test +threads +tng ${ACCE_IUSE}" |
360 |
- |
361 |
-CDEPEND=" |
362 |
- X? ( |
363 |
- x11-libs/libX11 |
364 |
- x11-libs/libSM |
365 |
- x11-libs/libICE |
366 |
- ) |
367 |
- blas? ( virtual/blas ) |
368 |
- cuda? ( >=dev-util/nvidia-cuda-toolkit-6.5.14 ) |
369 |
- opencl? ( virtual/opencl ) |
370 |
- fftw? ( sci-libs/fftw:3.0 ) |
371 |
- hwloc? ( sys-apps/hwloc ) |
372 |
- lapack? ( virtual/lapack ) |
373 |
- lmfit? ( sci-libs/lmfit ) |
374 |
- mkl? ( sci-libs/mkl ) |
375 |
- mpi? ( virtual/mpi ) |
376 |
- ${PYTHON_DEPS} |
377 |
- " |
378 |
-BDEPEND="${CDEPEND} |
379 |
- virtual/pkgconfig |
380 |
- doc? ( |
381 |
- app-doc/doxygen |
382 |
- $(python_gen_cond_dep ' |
383 |
- dev-python/sphinx[${PYTHON_MULTI_USEDEP}] |
384 |
- ') |
385 |
- media-gfx/mscgen |
386 |
- media-gfx/graphviz |
387 |
- dev-texlive/texlive-latex |
388 |
- dev-texlive/texlive-latexextra |
389 |
- media-gfx/imagemagick |
390 |
- )" |
391 |
-RDEPEND="${CDEPEND}" |
392 |
- |
393 |
-REQUIRED_USE=" |
394 |
- || ( single-precision double-precision ) |
395 |
- cuda? ( single-precision ) |
396 |
- cuda? ( !opencl ) |
397 |
- mkl? ( !blas !fftw !lapack ) |
398 |
- ${PYTHON_REQUIRED_USE}" |
399 |
- |
400 |
-DOCS=( AUTHORS README ) |
401 |
- |
402 |
-RESTRICT="!test? ( test )" |
403 |
- |
404 |
-if [[ ${PV} != *9999 ]]; then |
405 |
- S="${WORKDIR}/${PN}-${PV/_/-}" |
406 |
-fi |
407 |
- |
408 |
-pkg_pretend() { |
409 |
- [[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs" |
410 |
- use openmp && ! tc-has-openmp && \ |
411 |
- die "Please switch to an openmp compatible compiler" |
412 |
-} |
413 |
- |
414 |
-src_unpack() { |
415 |
- if [[ ${PV} != *9999 ]]; then |
416 |
- default |
417 |
- else |
418 |
- git-r3_src_unpack |
419 |
- if use test; then |
420 |
- EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \ |
421 |
- EGIT_BRANCH="${EGIT_BRANCH}" \ |
422 |
- EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\ |
423 |
- git-r3_src_unpack |
424 |
- fi |
425 |
- fi |
426 |
-} |
427 |
- |
428 |
-src_prepare() { |
429 |
- #notes/todos |
430 |
- # -on apple: there is framework support |
431 |
- |
432 |
- xdg_environment_reset #591952 |
433 |
- |
434 |
- cmake-utils_src_prepare |
435 |
- |
436 |
- use cuda && cuda_src_prepare |
437 |
- |
438 |
- GMX_DIRS="" |
439 |
- use single-precision && GMX_DIRS+=" float" |
440 |
- use double-precision && GMX_DIRS+=" double" |
441 |
- |
442 |
- if use test; then |
443 |
- for x in ${GMX_DIRS}; do |
444 |
- mkdir -p "${WORKDIR}/${P}_${x}" || die |
445 |
- cp -al "${WORKDIR}/regressiontests"* "${WORKDIR}/${P}_${x}/tests" || die |
446 |
- done |
447 |
- fi |
448 |
- |
449 |
- DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats" |
450 |
- |
451 |
- # try to create policy for imagemagik |
452 |
- mkdir -p ${HOME}/.config/ImageMagick |
453 |
- cat >> ${HOME}/.config/ImageMagick/policy.xml <<- EOF |
454 |
- <?xml version="1.0" encoding="UTF-8"?> |
455 |
- <!DOCTYPE policymap [ |
456 |
- <!ELEMENT policymap (policy)+> |
457 |
- !ATTLIST policymap xmlns CDATA #FIXED ''> |
458 |
- <!ELEMENT policy EMPTY> |
459 |
- <!ATTLIST policy xmlns CDATA #FIXED '' domain NMTOKEN #REQUIRED |
460 |
- name NMTOKEN #IMPLIED pattern CDATA #IMPLIED rights NMTOKEN #IMPLIED |
461 |
- stealth NMTOKEN #IMPLIED value CDATA #IMPLIED> |
462 |
- ]> |
463 |
- <policymap> |
464 |
- <policy domain="coder" rights="read | write" pattern="PS" /> |
465 |
- <policy domain="coder" rights="read | write" pattern="PS2" /> |
466 |
- <policy domain="coder" rights="read | write" pattern="PS3" /> |
467 |
- <policy domain="coder" rights="read | write" pattern="EPS" /> |
468 |
- <policy domain="coder" rights="read | write" pattern="PDF" /> |
469 |
- <policy domain="coder" rights="read | write" pattern="XPS" /> |
470 |
- </policymap> |
471 |
- EOF |
472 |
-} |
473 |
- |
474 |
-src_configure() { |
475 |
- local mycmakeargs_pre=( ) extra fft_opts=( ) |
476 |
- |
477 |
- #go from slowest to fastest acceleration |
478 |
- local acce="None" |
479 |
- use cpu_flags_x86_sse2 && acce="SSE2" |
480 |
- use cpu_flags_x86_sse4_1 && acce="SSE4.1" |
481 |
- use cpu_flags_x86_fma4 && acce="AVX_128_FMA" |
482 |
- use cpu_flags_x86_avx && acce="AVX_256" |
483 |
- use cpu_flags_x86_avx2 && acce="AVX2_256" |
484 |
- |
485 |
- #to create man pages, build tree binaries are executed (bug #398437) |
486 |
- [[ ${CHOST} = *-darwin* ]] && \ |
487 |
- extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF" |
488 |
- |
489 |
- if use fftw; then |
490 |
- fft_opts=( -DGMX_FFT_LIBRARY=fftw3 ) |
491 |
- elif use mkl && has_version "=sci-libs/mkl-10*"; then |
492 |
- fft_opts=( -DGMX_FFT_LIBRARY=mkl |
493 |
- -DMKL_INCLUDE_DIR="${MKLROOT}/include" |
494 |
- -DMKL_LIBRARIES="$(echo /opt/intel/mkl/10.0.5.025/lib/*/libmkl.so);$(echo /opt/intel/mkl/10.0.5.025/lib/*/libiomp*.so)" |
495 |
- ) |
496 |
- elif use mkl; then |
497 |
- local bits=$(get_libdir) |
498 |
- fft_opts=( -DGMX_FFT_LIBRARY=mkl |
499 |
- -DMKL_INCLUDE_DIR="$(echo /opt/intel/*/mkl/include)" |
500 |
- -DMKL_LIBRARIES="$(echo /opt/intel/*/mkl/lib/*${bits/lib}/libmkl_rt.so)" |
501 |
- ) |
502 |
- else |
503 |
- fft_opts=( -DGMX_FFT_LIBRARY=fftpack ) |
504 |
- fi |
505 |
- |
506 |
- if use lmfit; then |
507 |
- local lmfit_opts=( -DGMX_USE_LMFIT=EXTERNAL ) |
508 |
- else |
509 |
- local lmfit_opts=( -DGMX_USE_LMFIT=INTERNAL ) |
510 |
- fi |
511 |
- |
512 |
- mycmakeargs_pre+=( |
513 |
- "${fft_opts[@]}" |
514 |
- "${lmfit_opts[@]}" |
515 |
- -DGMX_X11=$(usex X) |
516 |
- -DGMX_EXTERNAL_BLAS=$(usex blas) |
517 |
- -DGMX_EXTERNAL_LAPACK=$(usex lapack) |
518 |
- -DGMX_OPENMP=$(usex openmp) |
519 |
- -DGMX_COOL_QUOTES=$(usex offensive) |
520 |
- -DGMX_USE_TNG=$(usex tng) |
521 |
- -DGMX_BUILD_MANUAL=$(usex doc) |
522 |
- -DGMX_HWLOC=$(usex hwloc) |
523 |
- -DGMX_DEFAULT_SUFFIX=off |
524 |
- -DGMX_SIMD="$acce" |
525 |
- -DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/" |
526 |
- -DBUILD_TESTING=$(usex test) |
527 |
- -DGMX_BUILD_UNITTESTS=$(usex test) |
528 |
- -DPYTHON_EXECUTABLE="${EPREFIX}/usr/bin/${EPYTHON}" |
529 |
- ${extra} |
530 |
- ) |
531 |
- |
532 |
- for x in ${GMX_DIRS}; do |
533 |
- einfo "Configuring for ${x} precision" |
534 |
- local suffix="" |
535 |
- #if we build single and double - double is suffixed |
536 |
- use double-precision && use single-precision && \ |
537 |
- [[ ${x} = "double" ]] && suffix="_d" |
538 |
- local p |
539 |
- [[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF" |
540 |
- local cuda=( "-DGMX_GPU=OFF" ) |
541 |
- [[ ${x} = "float" ]] && use cuda && \ |
542 |
- cuda=( "-DGMX_GPU=ON" ) |
543 |
- local opencl=( "-DGMX_USE_OPENCL=OFF" ) |
544 |
- use opencl && opencl=( "-DGMX_USE_OPENCL=ON" ) cuda=( "-DGMX_GPU=ON" ) |
545 |
- mycmakeargs=( |
546 |
- ${mycmakeargs_pre[@]} ${p} |
547 |
- -DGMX_MPI=OFF |
548 |
- -DGMX_THREAD_MPI=$(usex threads) |
549 |
- -DGMXAPI=$(usex gmxapi) |
550 |
- "${opencl[@]}" |
551 |
- "${cuda[@]}" |
552 |
- "$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")" |
553 |
- -DGMX_BINARY_SUFFIX="${suffix}" |
554 |
- -DGMX_LIBS_SUFFIX="${suffix}" |
555 |
- ) |
556 |
- BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure |
557 |
- [[ ${CHOST} != *-darwin* ]] || \ |
558 |
- sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die |
559 |
- use mpi || continue |
560 |
- einfo "Configuring for ${x} precision with mpi" |
561 |
- mycmakeargs=( |
562 |
- ${mycmakeargs_pre[@]} ${p} |
563 |
- -DGMX_THREAD_MPI=OFF |
564 |
- -DGMX_MPI=ON |
565 |
- -DGMX_OPENMM=OFF |
566 |
- -DGMXAPI=OFF |
567 |
- "${opencl[@]}" |
568 |
- "${cuda[@]}" |
569 |
- -DGMX_BUILD_MDRUN_ONLY=ON |
570 |
- -DBUILD_SHARED_LIBS=OFF |
571 |
- -DGMX_BUILD_MANUAL=OFF |
572 |
- -DGMX_BINARY_SUFFIX="_mpi${suffix}" |
573 |
- -DGMX_LIBS_SUFFIX="_mpi${suffix}" |
574 |
- ) |
575 |
- BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_src_configure |
576 |
- [[ ${CHOST} != *-darwin* ]] || \ |
577 |
- sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}_mpi/gentoo_rules.cmake" || die |
578 |
- done |
579 |
-} |
580 |
- |
581 |
-src_compile() { |
582 |
- for x in ${GMX_DIRS}; do |
583 |
- einfo "Compiling for ${x} precision" |
584 |
- BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
585 |
- cmake-utils_src_compile |
586 |
- # not 100% necessary for rel ebuilds as available from website |
587 |
- if use doc; then |
588 |
- BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
589 |
- cmake-utils_src_compile manual |
590 |
- fi |
591 |
- use mpi || continue |
592 |
- einfo "Compiling for ${x} precision with mpi" |
593 |
- BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\ |
594 |
- cmake-utils_src_compile |
595 |
- done |
596 |
-} |
597 |
- |
598 |
-src_test() { |
599 |
- for x in ${GMX_DIRS}; do |
600 |
- BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
601 |
- cmake-utils_src_make check |
602 |
- done |
603 |
-} |
604 |
- |
605 |
-src_install() { |
606 |
- for x in ${GMX_DIRS}; do |
607 |
- BUILD_DIR="${WORKDIR}/${P}_${x}" \ |
608 |
- cmake-utils_src_install |
609 |
- if use doc; then |
610 |
- newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf" |
611 |
- fi |
612 |
- use mpi || continue |
613 |
- BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \ |
614 |
- cmake-utils_src_install |
615 |
- done |
616 |
- |
617 |
- if use tng; then |
618 |
- insinto /usr/include/tng |
619 |
- doins src/external/tng_io/include/tng/*h |
620 |
- fi |
621 |
- # drop unneeded stuff |
622 |
- rm "${ED}"/usr/bin/GMXRC* || die |
623 |
- for x in "${ED}"/usr/bin/gmx-completion-*.bash ; do |
624 |
- local n=${x##*/gmx-completion-} |
625 |
- n="${n%.bash}" |
626 |
- cat "${ED}"/usr/bin/gmx-completion.bash "$x" > "${T}/${n}" || die |
627 |
- newbashcomp "${T}"/"${n}" "${n}" |
628 |
- done |
629 |
- rm "${ED}"/usr/bin/gmx-completion*.bash || die |
630 |
- readme.gentoo_create_doc |
631 |
-} |
632 |
- |
633 |
-pkg_postinst() { |
634 |
- einfo |
635 |
- einfo "Please read and cite:" |
636 |
- einfo "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). " |
637 |
- einfo "https://dx.doi.org/10.1021/ct700301q" |
638 |
- einfo |
639 |
- readme.gentoo_print_elog |
640 |
-} |